%% inproceedings : issue d'une conf.
%% Champs requis : author, title, booktitle, year
%% Champs optionnels : editor, pages, organization, publisher, address, month, note, key

%%%%%% Sujet

@misc{sujet,
author  = {Pascal Ferraro},
title   = {Comparaison d’arborescences non ordonnées},
year    = {2011-2012},
note    = {Bordeaux I, Sujet d'ABV},
url     = {https://www.labri.fr/perso/ferraro/Master/2011-2012/Projet-ABV2}
}

% sujet Rachid/Romarick
@misc{sujetARN,
author  = {Pascal Ferraro},
title   = {Comparaison de structures secondaires d’ARN},
year    = {2011-2012},
note    = {Bordeaux I, Sujet d'ABV},
url     = {https://www.labri.fr/perso/ferraro/Master/2011-2012/Projet-ABV1}
}

% Multiscale Tree Graph
@article{godin98,
  author       = {Godin, C. and Caraglio, Y.},
  title        = {A multiscale model of plant topological structures},
  journal      = {Journal of Theoretical Biology},
  volume       = {191},
  pages        = {1-46},
  year         = {1998},
  url          = {http://www-sop.inria.fr/virtualplants/Publications/1998/GC98}
}

% problème distance d'édition - contrainte de Zhang 
@article{zhang96,
  author    = {Kaizhong Zhang},
  title     = {A Constrained Edit Distance Between Unordered Labeled Trees},
  journal   = {Algorithmica},
  volume    = {15},
  number    = {3},
  year      = {1996},
  pages     = {205-222}
}

% site officiel Tulip
@misc{tulip,
title  = {Tulip, Better Visualization Through Research},
howpublished = {\url{http://tulip.labri.fr/TulipDrupal/}}
}

% site officiel openalea
@misc{openalea,
title  = {OpenAlea, Software Environment for Plant Modeling},
howpublished = {\url{http://openalea.gforge.inria.fr/}}
}

%
@phdthesis{theseferraro,
author = {P. Ferraro},
title  = {Méthodes algorithmiques de comparaison d'arborescences. Applications à la comparaison de l'architecture des plantes},
school = { INPT, Toulouse },
year   = {2000},
}

% 
@phdthesis{theseouangraoua,
author = {A. Ouangraoua},
title  = {Développement d'outils conceptuels et algorithmiques pour l'analyse de structures biologiques arborescentes.},
school = { ACI, Nouvelle interface des Mathématiques },
year   = {2007},
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% travaux Ferraro Godin sur distance édition en modélisation de plantes

@techreport{ferraro98,
    author = {Ferraro, Pascal},
    citeulike-article-id = {576909},
    institution = {Cirad},
    title = {Une m{\'e}thode de comparaison structurelle d'arborescences non ordonn{\'e}es},
    year = {1998}
}

@inproceedings\{FG98a,
  author       = "Ferraro, Pascal and Godin, Christophe",
  title        = "Un algorithme de comparaison d'arborescences non ordonnées appliqué à la comparaison de la structure topologique des plantes",
  booktitle    = "SFC98 : Soci\'et\'e Francophone de classification",
  pages        = "77-81",
  year         = "1998",
  address      = "Montpellier (France)",
  url          = "http://www.labri.fr/publications/mabiovis/1998/FG98a"
}

% implémentation de l'article de Zhang
% "adaptation of an algorithm for comparing rooted tree graphs"
@article{ FerraroGodin00,
	author = {{Pascal Ferraro} and {Christophe Godin}},
	title = {A distance measure between plant architectures},
	url= "http://dx.doi.org/10.1051/forest:2000134",
	journal = {Ann. For. Sci.},
	year = 2000,
	volume = 57,
	number = 5,
	pages = "445-461"
}

@article{FerraroGodin03,
    title = {{An edit distance between quotiented graphs}},
    author = {Ferraro, Pascal and Godin, Christophe},
    language = {Anglais},
    affiliation = {Laboratoire Bordelais de Recherche en Informatique - LaBRI , Virtual Plants - VP},
    pages = {1-39},
    journal = {Algorithmica},
    volume = {36},
    year = {2003},
}
%%%%%%%%%%%%%  approche architecturale / topologique

% article fondateur 1
@book{ HalleOldeman70,
author        = { Francis Halle, R. Oldeman },
title         = { Essai sur l'architecture et la dynamique de croissance des arbres tropicaux},
publisher     = { Masson, Paris },
year          = { 1970 },
}

% article fondateur 2
@book{ HalleOldemanTomlison78,
author    = { Francis Halle, R. Oldeman et P.B. Tomlinson },
title     = { Tropical trees and forests : an architectural analysis },
publisher = { New York : Springer-Verlag, Berlin},
year      = { 1978 },
isbn      = { 0387084940 }
}

% extension concept architecture aux conifères
@article {edelin81,
author    = {C. Edelin},
title     = {Quelques aspects de l'architecture végétative des Conifères},
book      = {Bulletin de la Société botanique de France},
volume    = {28},
publisher = {La Société, Paris},
year      = {1981},
pages     = {177-188}
}

% architecture selon Godin
@article{godin00,
    author = {Godin, Christophe},
    journal = {Annals of Forest Science},
    pages = {413--438},
    posted-at = {2009-12-14 11:18:42},
    priority = {4},
    title = {{Representing and encoding plant architecture: A review}},
    volume = {57},
    year = {2000}
}


% extension concept d'architecture à l'herbe
@book{jeannoda1977,
  title={Contribution {\`a} l'{\'e}tude de l'architecture des herbes},
  author={Jeannoda-Robinson, V.},
  url={http://books.google.fr/books?id=rb1CYgEACAAJ},
  year={1977},
  publisher={Universit{\'e} des Sciences et Techniques du Languedoc}
}

% extenstion concept archi à des lianes
@article{cremers73,
  title = {{A}rchitecture de quelques lianes d'{A}frique tropicale},
  author = {{C}remers, {G}eorges},
  language = {{FR}},
  journal = {{C}andollea},
  volume = {28},
  pages = {249--280},
  ISSN = {0373-2967},
  year = {1973}
}

% review architecture
@article{barthelemy07, 
title    ={Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny.},
volume   ={99}, 
url      ={http://www.ncbi.nlm.nih.gov/pubmed/17218346}, 
number   ={3}, journal={Annals of Botany}, 
publisher={Oxford University Press}, 
author   ={Barthélémy, Daniel and Caraglio, Yves}, 
year     ={2007}, 
pages    ={375-407}
}


% livre fondateur / étude developpement plantes
@book{goethe1790,
  title={Versuch die Metamorphose der Pflanzen zu erkl{\"a}ren},
  author={Goethe, J.W.},
  year={1790}
}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Distance / Comparaison
% origine édition distance / comparaison de string
@article{WagnerFischer74,
 author = {Wagner, Robert A. and Fischer, Michael J.},
 title = {The String-to-String Correction Problem},
 journal = {J. ACM},
 volume = {21},
 issue = {1},
 month = {January},
 year = {1974},
 issn = {0004-5411},
 pages = {168--173},
 numpages = {6},
 acmid = {321811},
 publisher = {ACM}
} 

% origine local similarity
@article{SmithWaterman81,
    author = {Smith, T. F. and Waterman, M. S.},
    day = {25},
    journal = {Journal of molecular biology},
    month = mar,
    number = {1},
    pages = {195--197},
    priority = {2},
    title = {{Identification of common molecular subsequences.}},
    volume = {147},
    year = {1981}
}

@article{selkow77,
    author = {Selkow, S.},
    journal = {Information Processing Letters},
    month = dec,
    number = {6},
    pages = {184--186},
    title = {{The tree-to-tree editing problem}},
    volume = {6},
    year = {1977}
}


% état de l'art 2005 sur la distance d'édition / pas cité ... à voir
@article{bille05,
    author = {Philip Bille},
    title = {A survey on tree edit distance and related problems},
    journal = {Theor. Comput. Sci},
    year = {2005},
    volume = {337},
    pages = {217-239}
}

% ordered labeled tree en O(n6)
@article{tai79,
 author = {Tai, Kuo-Chung},
 title = {The Tree-to-Tree Correction Problem},
 journal = {J. ACM},
 volume = {26},
 issue = {3},
 month = {July},
 year = {1979},
 pages = {422--433},
 numpages = {12},
 publisher = {ACM, NYC},
}
 
% ordered labeled tree en O(n3)
@inproceedings{demaine07,
    author = {Erik D. Demaine and Shay Mozes and Benjamin Rossman and Oren Weimann},
    title = {An optimal decomposition algorithm for tree edit distance},
    booktitle = {In Proceedings of the 34th International Colloquium on Automata, Languages and Programming (ICALP},
    year = {2007},
    pages = {146--157}
}

% preuve distance d'édition sur arbre non ordonné NP-Complet
@article{zhang1992,
 author = {Zhang, Kaizhong and Statman, Rick and Shasha, Dennis},
 title = {On the editing distance between unordered labeled trees},
 journal = {Inf. Process. Lett.},
 volume = {42},
 issue = {3},
 month = {May},
 year = {1992},
 issn = {0020-0190},
 pages = {133--139},
 numpages = {7},
 acmid = {136115},
 publisher = {Elsevier North-Holland, Inc.}
}

% preuve distance d'édition sur arbre non ordonné MAX SNP
@article{zhang1994,
 author = {Zhang, Kaizhong and Jiang, Tao},
 title = {Some MAX SNP-hard results concerning unordered labeled trees},
 journal = {Inf. Process. Lett.},
 volume = {49},
 issue = {5},
 month = {March},
 year = {1994},
 issn = {0020-0190},
 pages = {249--254},
 numpages = {6},
 acmid = {177380},
 publisher = {Elsevier North-Holland, Inc.},
} 

% algo édition distance cas particulier
@inproceedings{halldorsson1996,
 author = {Halld\'{o}rsson, Magn\'{u}s M. and Tanaka, Keisuke},
 title = {Approximation and Special Cases of Common Subtrees and Editing Distance},
 booktitle = {Proceedings of the 7th International Symposium on Algorithms and Computation},
 series = {ISAAC '96},
 year = {1996},
 isbn = {3-540-62048-6},
 pages = {75--84},
 numpages = {10},
 acmid = {688731},
 publisher = {Springer-Verlag},
} 

% fameux algo de Shasha et Zhang - article de Zhang précédent celui du sujet
@article{ShashaZhang94,
  added-at = {2010-12-17T00:00:00.000+0100},
  author = {Shasha, Dennis and Wang, Jason Tsong-Li and Zhang, Kaizhong and Shih, Frank Y.},
  journal = {IEEE Transactions on Systems, Man, and Cybernetics},
  number = 4,
  pages = {668-678},
  title = {Exact and approximate algorithms for unordered tree matching.},
  volume = 24,
  year = 1994
}

% ordered rooted tree - adaptation Zhang/Shasha 89
@article{ouangraoua07,
 author = {Ouangraoua, Aida and Ferraro, Pascal and Tichit, Laurent and Dulucq, Serge},
 title = {Local similarity between quotiented ordered trees},
 journal = {J. of Discrete Algorithms},
 volume = {5},
 issue = {1},
 month = {March},
 year = {2007},
 pages = {23--35},
 numpages = {13},
 publisher = {Elsevier Science Publishers B. V.},
 address = {Amsterdam, The Netherlands, The Netherlands},
} 

@article{OuangraouaFerraro2009,
 author = {Ouangraoua, A. and Ferraro, P.},
 title = {A constrained edit distance algorithm between semi-ordered trees},
 journal = {Theor. Comput. Sci.},
 volume = {410},
 issue = {8-10},
 month = {March},
 year = {2009},
 issn = {0304-3975},
 pages = {837--846},
 numpages = {10},
} 

% perspective / article 2011
@article{akutsu2011,
 author = {Akutsu, Tatsuya and Fukagawa, Daiji and Takasu, Atsuhiro and Tamura, Takeyuki},
 title = {Exact algorithms for computing the tree edit distance between unordered trees},
 journal = {Theor. Comput. Sci.},
 issue_date = {February, 2011},
 volume = {412},
 issue = {4-5},
 month = {February},
 year = {2011},
 issn = {0304-3975},
 pages = {352--364},
 numpages = {13},
 acmid = {1923327},
 publisher = {Elsevier Science Publishers Ltd.},
} 


@article{edmonskarp72,
 author = {Edmonds, Jack and Karp, Richard M.},
 title = {Theoretical Improvements in Algorithmic Efficiency for Network Flow Problems},
 journal = {J. ACM},
 volume = {19},
 issue = {2},
 month = {April},
 year = {1972},
 issn = {0004-5411},
 pages = {248--264},
 numpages = {17},
 acmid = {321699},
 publisher = {ACM},
} 